Symmetric expression of ohnologs encoding conserved antiviral responses in tetraploid common carp suggest absence of subgenome dominance after whole genome duplication

Allopolyploids often experience subgenome dominance, with one subgenome showing higher levels of gene expression and greater gene retention. Here, we address the functionality of both subgenomes of allotetraploid common carp (Cyprinus carpio) by analysing a functional network of interferon-stimulated genes (ISGs) crucial in anti-viral immune defence. As an indicator of subgenome dominance we investigated retainment of a core set of ohnologous ISGs. To facilitate our functional genomic analysis a high quality genome was assembled (WagV4.0). Transcriptome data from an in vitro experiment mimicking a viral infection was used to infer ISG expression. Transcriptome analysis confirmed induction of 88 ISG ohnologs on both subgenomes. In both control and infected states, average expression of ISG ohnologs was comparable between the two subgenomes. Also, the highest expressing and most inducible gene copies of an ohnolog pair could be derived from either subgenome. We found no strong evidence of subgenome dominance for common carp.

[Fish-caused illness: notify food-related outbreaks to the Municipal Health Services]

BACKGROUND

When two or more people fall ill after eating the same food, this is called an outbreak of food poisoning or food-related infection. In the Netherlands, physicians have to notify the Municipal Health Services (GGD) of such outbreaks. The GGD informs the Netherlands Food and Consumer Product Safety Authority (NVWA).

CASE DESCRIPTION

Two clusters of scombroid poisoning (histamine poisoning in this case after eating tuna) occurred in one month. Due to the quick reporting of patients by physicians, the GGD and the NVWA immediately tracked down the source. In both clusters the NVWA confirmed high histamine levels in tuna. In reaction to these findings and the first cluster, the supplier recalled the tuna batch. This may have prevented other cases of food poisoning. In the second cluster, the implicated tuna batch had already been sold.

CONCLUSION

Timely notification by physicians of food poisoning or food-related outbreaks to the GGD enables swift tracing of the source and appropriate measures by the GGD and the NVWA..

A full-body transcriptome and proteome resource for the European common carp

Background

The common carp (Cyprinus carpio) is the oldest, most domesticated and one of the most cultured fish species for food consumption. Besides its economic importance, the common carp is also highly suitable for comparative physiological and disease studies in combination with the animal model zebrafish (Danio rerio). They are genetically closely related but offer complementary benefits for fundamental research, with the large body mass of common carp presenting possibilities for obtaining sufficient cell material for advanced transcriptome and proteome studies.

Results

Here we have used 19 different tissues from an F1 hybrid strain of the common carp to perform transcriptome analyses using RNA-Seq. For a subset of the tissues we also have performed deep proteomic studies. As a reference, we updated the European common carp genome assembly using low coverage Pacific Biosciences sequencing to permit high-quality gene annotation. These annotated gene lists were linked to zebrafish homologs, enabling direct comparisons with published datasets. Using clustering, we have identified sets of genes that are potential selective markers for various types of tissues. In addition, we provide a script for a schematic anatomical viewer for visualizing organ-specific expression data.

Conclusions

The identified transcriptome and proteome data for carp tissues represent a useful resource for further translational studies of tissue-specific markers for this economically important fish species that can lead to new markers for organ development. The similarity to zebrafish expression patterns confirms the value of common carp as a resource for studying tissue-specific expression in cyprinid fish. The availability of the annotated gene set of common carp will enable further research with both applied and fundamental purposes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3038-y) contains supplementary material, which is available to authorized users.

Durable efficacy of liraglutide in patients with type 2 diabetes and pronounced insulin-associated weight gain: 52-week results from the Effect of Liraglutide on insulin-associated wEight GAiN in patients with Type 2 diabetes' (ELEGANT) randomized controlled trial

BACKGROUND

Pronounced weight gain frequently complicates insulin therapy in patients with type 2 diabetes (T2DM). We have previously reported that addition of liraglutide for 26 weeks can reverse insulin-associated weight gain, decrease insulin dose and improve glycaemic control, as compared with continuation of standard insulin treatment.

OBJECTIVES

To investigate whether the beneficial effects of liraglutide are sustained up to 52 weeks and whether similar effects could be obtained when liraglutide is added 6 months later.

METHODS

Adult T2DM patients with ≥ 4% weight gain within 16 months of insulin therapy completing the first 26-week trial period of open-label addition of liraglutide 1.8 mg day(-1) (n = 26) versus continuation of standard insulin therapy (n = 24) were all treated with liraglutide for another 26 weeks. Results were analysed according to the intention-to-treat principle.

RESULTS

Overall, 24 (92%) and 18 (75%) patients originally assigned to liraglutide and standard therapy, respectively, completed the study. Addition of liraglutide decreased body weight to a similar extend when given in the first 26 weeks (liraglutide group) or second 26 weeks (original standard therapy group): -4.4 vs. -4.3 kg (difference -0.32 kg, 95% confidence interval -2.2 to 1.6 kg; P = 0.74). Similar results were also seen in the two groups with regard to decrease in haemoglobin A1c (HbA1c ) (-0.77 vs. -0.66%; P = 0.23) and insulin dose (-28 vs. -26 U day(-1) ; P = 0.32). In both groups, 22% of patients could discontinue insulin. Continuation of liraglutide until 52 weeks led to sustained effects on body weight, HbA1c and insulin-dose requirements.

CONCLUSION

In T2DM patients with pronounced insulin-associated weight gain, addition of liraglutide within 2 years leads to sustained reversal of body weight, improved glycaemic control and decrease in insulin dose. Thus, liraglutide offers a valuable therapeutic option.

Biological warfare, bioterrorism, and biocrime

Biological weapons achieve their intended target effects through the infectivity of disease-causing infectious agents. The ability to use biological agents in warfare is prohibited by the Biological and Toxin Weapon Convention. Bioterrorism is defined as the deliberate release of viruses, bacteria or other agents used to cause illness or death in people, but also in animals or plants. It is aimed at creating casualties, terror, societal disruption, or economic loss, inspired by ideological, religious or political beliefs. The success of bioterroristic attempts is defined by the measure of societal disruption and panic, and not necessarily by the sheer number of casualties. Thus, making only a few individuals ill by the use of crude methods may be sufficient, as long as it creates the impact that is aimed for. The assessment of bioterrorism threats and motives have been described before. Biocrime implies the use of a biological agent to kill or make ill a single individual or small group of individuals, motivated by revenge or the desire for monetary gain by extortion, rather than by political, ideological, religious or other beliefs. The likelihood of a successful bioterrorist attack is not very large, given the technical difficulties and constraints. However, even if the number of casualties is likely to be limited, the impact of a bioterrorist attack can still be high. Measures aimed at enhancing diagnostic and therapeutic capabilities and capacities alongside training and education will improve the ability of society to combat 'regular' infectious diseases outbreaks, as well as mitigating the effects of bioterrorist attacks.

Start of insulin therapy in patients with type 2 diabetes mellitus promotes the influx of macrophages into subcutaneous adipose tissue

AIMS/HYPOTHESIS

Insulin therapy in patients with type 2 diabetes mellitus is accompanied by weight gain characterised by an increase in abdominal fat mass. The expansion of adipose tissue mass is generally paralleled by profound morphological and inflammatory changes. We hypothesised that the insulin-associated increase in fat mass would also result in changes in the morphology of human subcutaneous adipose tissue and in increased inflammation, especially when weight gain was excessive.

METHODS

We investigated the effects of weight gain on adipocyte size, macrophage influx, and mRNA expression and protein levels of key inflammatory markers within the adipose tissue in patients with type 2 diabetes mellitus before and 6 months after starting insulin therapy.

RESULTS

As expected, insulin therapy significantly increased body weight. At the level of the subcutaneous adipose tissue, insulin treatment led to an influx of macrophages. When comparing patients gaining no or little weight with patients gaining >4% body weight after 6 months of insulin therapy, both subgroups displayed an increase in macrophage influx. However, individuals who had gained weight had higher protein levels of monocyte chemoattractant protein-1, TNF-α and IL-1β after 6 months of insulin therapy compared with those who had not gained weight.

CONCLUSIONS/INTERPRETATION

We conclude that insulin therapy in patients with type 2 diabetes mellitus improved glycaemic control but also induced body weight gain and an influx of macrophages into the subcutaneous adipose tissue. In patients characterised by a pronounced insulin-associated weight gain, the influx of macrophages into the adipose tissue was accompanied by a more pronounced inflammatory status.

TRIAL REGISTRATION

ClinicalTrials.gov: NCT00781495.

FUNDING

The study was funded by European Foundation for the Study of Diabetes and the Dutch Diabetes Research Foundation.

Autophagy activity is up-regulated in adipose tissue of obese individuals and modulates proinflammatory cytokine expression

Autophagy, an evolutionary conserved process aimed at recycling damaged organelles and protein aggregates in the cell, also modulates proinflammatory cytokine production in peripheral blood mononuclear cells. Because adipose tissue inflammation accompanied by elevated levels of proinflammatory cytokines is characteristic for the development of obesity, we hypothesized that modulation of autophagy alters adipose tissue inflammatory gene expression and secretion. We tested our hypothesis using ex vivo and in vivo studies of human and mouse adipose tissue. Levels of the autophagy marker LC3 were elevated in sc adipose tissue of obese vs. lean human subjects and positively correlated to both systemic insulin resistance and morphological characteristics of adipose tissue inflammation. Similarly, autophagic activity levels were increased in adipose tissue of obese and insulin resistant animals as compared with lean mice. Inhibition of autophagy by 3-methylalanine in human and mouse adipose tissue explants led to a significant increase in IL-1β, IL-6, and IL-8 mRNA expression and protein secretion. Noticeably, the enhancement in IL-1β, IL-6, and keratinocyte-derived chemoattractant (KC) by inhibition of autophagy was more robust in the presence of obesity. Similar results were obtained by blocking autophagy using small interfering RNA targeted to ATG7 in human Simpson-Golabi-Behmel syndrome adipocytes. Our results demonstrate that autophagy activity is up-regulated in the adipose tissue of obese individuals and inhibition of autophagy enhances proinflammatory gene expression both in adipocytes and adipose tissue explants. Autophagy may function to dampen inflammatory gene expression and thereby limit excessive inflammation in adipose tissue during obesity.

Contribution of change in glycosylated haemoglobin to insulin-associated weight gain: results of a longitudinal study in type 2 diabetic patients

To investigate the contribution of glycosylated haemoglobin change (HbA1c) on body weight in patients with type 2 diabetes after start of insulin therapy. We analysed 122 individual weight-profiles in relation to the change in HbA1c per se in these patients up to 36 months after the start of insulin therapy. Data were analysed separately for the first 9 months after commencement of insulin therapy and for the period thereafter. Within the first 9 months of insulin therapy mean body weight increased by 0.52 kg per month. HbA1c decreased from 9.9 ± 1.8 to 7.9 ± 1.3%. Only 12% of the initial weight gain could be attributed to the change in HbA1c. Furthermore, the mean monthly increase in body weight gain was reduced by 0.006 kg for every 1 kg higher body weight at baseline. From 9 to 36 months after start of insulin therapy, body weight increased by 0.1 kg/month, which was independent of change in HbA1c. Improvement of glycaemic control per se contributes little to initial weight gain after start of insulin therapy in patients with T2DM. After 9 months of insulin treatment, weight gain is unrelated to change in glycosylated haemoglobin. Other factors have to be responsible for weight gain after start of insulin therapy.

Time-space translation: a developmental principle

We review a recently discovered developmental mechanism. Anterior-posterior positional information for the vertebrate trunk is generated by sequential interactions between a timer in the early nonorganizer mesoderm (NOM) and the Spemann organizer (SO). The timer is characterized by temporally collinear activation of a series of Hox genes in the early ventral and lateral mesoderm (i.e., the NOM) of the Xenopus gastrula. This early Hox gene expression is transient, unless it is stabilized by signals from the SO. The NOM and the SO undergo timed interactions due to morphogenetic movements during gastrulation, which lead to the formation of an anterior-posterior axial pattern and stable Hox gene expression. When separated from each other, neither the NOM nor the SO is able to induce anterior-posterior pattern formation of the trunk. We present a model describing that the NOM acquires transiently stable hox codes and spatial collinearity, and that morphogenetic movements then continually bring new cells from the NOM within the range of SO signals that cause transfer of the mesodermal pattern to a stable pattern in neurectoderm and, thereby, create patterned axial structures. In doing so, the age of the NOM, but not the age of the SO, defines positional values along the anterior-posterior axis. We postulate that the temporal information from the NOM is linked to mesodermal Hox expression. The role of the SO for trunk patterning turns out to be the induction of neural tissue as prerequisite for neural hox patterning. Apparently, development of a stable anterior-posterior pattern requires neural hox patterning. We believe that this mechanism represents a developmental principle.

Pronounced weight gain in insulin-treated patients with type 2 diabetes mellitus is associated with an unfavourable cardiometabolic risk profile

Pronounced weight gain after start of insulin therapy in patients with type 2 diabetes mellitus (T2DM) may offset beneficial effects conferred by the improvement of glycaemic control. This hypothesis was tested by comparing the cardiometabolic risk profile of a group of type 2 diabetes patients with a marked increase in body weight ('gainers) after the start of insulin treatment and a similar group without any or only minimal weight gain ('non-gainers'). In a cross-sectional study, we compared two predefined groups of patients with T2DM who had been on insulin therapy for a mean of 4.0 years: 'gainers' vs 'non-gainers'. Cardiometabolic risk was assessed by measuring fat content and distribution (physical examination, bioelectrical impedance analysis, dual energy X-ray absorption, and magnetic resonance imaging), liver fat content (magnetic resonance spectroscopy), physical activity levels (Sensewear® armband) and plasma markers. Each subgroup consisted of 14 patients. Gainers had significantly more total body and trunk fat (especially subcutaneous fat) compared with no-gainers. Gainers had similar liver fat content, and slightly higher levels of fat hormones. Furthermore, gainers performed significantly less physical activity. Lastly, gainers had higher total cholesterol, low-density lipoprotein cholesterol, and alanine aminotransferase levels with similar cholesterol-lowering treatment. Patients with T2DM who show pronounced weight gain during insulin therapy have a less favourable cardiometabolic risk profile compared with patients who show no or minimal weight gain.

Status epilepticus caused by a myxoedema coma

The case of a 63-year-old woman who presented with status epilepticus, coma and hypoventilation is reported. A primary neurological cause was considered. Hypothermia led to further investigations and a diagnosis of severe hypothyroidism. The neurological complications of hyperthyriodism include alteration in mental status with slowness, decreased concentration and lethargy, headache, cranial nerve palsies, dysarthria, hoarseness, myopathy, neuropathy, reflex changes, ataxia, and psychotic episodes. Our patient suffered from a rare consequence of severe hypothyroidism presenting with status epilepticus and she died despite treatment. To our knowledge this is the second patient to be reported with myxoedema coma with this kind of presentation. Despite therapeutic options, there is a high mortality rate.

Biochemical differences between three subcell-lines derived from SV40-transformed hamster lens cells

Clones derived from SV40-transformed hamster lens cells have at least three different stable morphologies. Biochemical differences between the three cell types that become detectable after transfection of the alpha A-crystallin gene do exist at the level of alpha B-crystallin and small heat shock protein (HSP27) expression. Furthermore one cell type is capable of alternative splicing of the hamster alpha A-crystallin gene, whereas another one cannot express alpha AIns-crystallin.

Protein degradation by Prevotella intermedia and Actinomyces meyeri supports the growth of non-protein-cleaving oral bacteria in serum

The proteolytic activities of oral bacteria are thought to play an important role in the aetiology of dental abscesses. Bacteria-derived proteases may contribute to tissue destruction, and are likely to impair host defence by degrading immunoglobulins and complement. Degraded periodontal tissue and tissue fluid are likely to constitute essential sources of nutrients in the abscess. Tissue fluid, which is derived from serum, is rich in protein and poor in carbohydrate, suggesting that breakdown of protein and fermentation of amino acids is a crucial step to generate energy for growth of the microflora. The number of oral bacterial species that perform hydrolytic cleavage of protein into polypeptides, the first step in protein degradation, is relatively small compared to the large majority of peptidase-producing species. In this study, we therefore investigated the growth-promoting effect of proteinase-producing species like Prevotella intermedia and Actinomyces meyeri on the growth of some non-proteinase producing bacteria in mixed cultures. We used serum as a substitute for the supposed natural substrate of the abscess microflora. The breakdown of serum proteins was investigated using capillary electrophoresis. Poor growth was found in mono- and mixed cultures of non-proteinase producing species Eubacterium lentum, Fusobacterium nucleatum. Peptostreptococcus micros, and Streptococcus intermedius. The presence of P. intermedia in mixed cultures strongly enhanced growth of these 4 species, according to the hypothesis that the growth of the mixed cultures was peptide-limited. The enhanced growth of P. intermedia in pronase-digested serum indicated peptide-limited growth of this organism in serum, despite its production of proteinase. We found that growth of monocultures of Actinomyces meyeri was poor. In contrast, A. meyeri grew well in mixed cultures and its presence stimulated growth of F. nucleatum and P. micros, suggesting a synergistic relationship. The growth of mono- and mixed cultures was investigated using one representative strain of each species. Thus, there is a small risk of having selected unique strains. Proteinase inhibitors reduced the growth of Porphyromonas gingivalis, Prevotella nigrescens, and P. intermedia in trypticase peptone-yeast extract medium with, and without, IgG. Our study indicated that proteinase-producing organisms play a key role in mixed cultures of oral bacteria in human serum by providing polypeptides for growth. This may explain their association with dental abscesses.

The importance of immunoglobulin-breakdown supporting the growth of bacteria in oral abscesses

Oral bacteria play an important rôle in the causation of oro-facial abscesses. However, they can also be involved in brain, liver and lung abscesses. To persist, it is essential that these bacteria can grow on those sites. The main source of nutrients for growth in abscesses is likely to be tissue exudate, which is rich in serum-derived proteins, and relatively poor in free amino acids and carbohydrates. Degradation of intact proteins seems a crucial step in providing the peptides necessary for energy generation. The aim of this study was to investigate the capacity of microorganisms from asscesses to degrade serum proteins, in particular immunoglobulins. To this end, samples were taken by aspiration from 16 odontogenic abscesses. It was found that pus from abscesses differed strongly in the concentration of viable bacterial cells. The ability of the abscess microflora to degrade serum proteins was investigated after growth of the sample in heat-inactivated human serum. The microflora from abscesses with a high concentration (n = 10) of bacteria strongly degraded immunoglobulins, whereas breakdown of immunoglobulins was virtually absent after growth of the microflora from low-bacterial concentration (n = 6) abscesses. Bacteriological analyses revealed the presence of at least one proteinase-producing species, like Porphyromonas, black-pigmented Prevotella species, or Actinomyces meyeri, in abscesses with a high density of bacteria, but not in those with low bacterial density. The results indicate that the capacity to degrade intact proteins, in particular immunoglobulins, is a major determinant of bacterial growth in abscesses.

A novel human c-sis mRNA species is transcribed from a promoter in c-sis intron 1 and contains the code for an alternative PDGF B-like protein

The human platelet-derived growth factor (PDGF) B chain precursor is usually translated from a 3.5 kb c-sis/PDGF B gene transcript. The first exon of the c-sis/gene contains the code for the signal peptide of the PDGF B chain precursor, preceded by a 1 kb long untranslated sequence with potent translation inhibitory activity. In this paper we show that a novel 2.6 kb c-sis mRNA present in the human choriocarcinoma cell line JEG-3 initiates at an alternative exon 1, which we refer to as exon 1a. The 90 bp long exon 1a is located in the center of the first intron of the gene. It coincides with a very pronounced DNase-I-hypersensitive site and is preceded by a functional promoter. Of the three ATG codons present in exon 1a, the third one perfectly matches the criteria of a consensus start codon. It initiates an open reading frame that is continuous with the code for the PDGF B chain precursor but lacks the code for a signal peptide. We conclude that this novel 2.6 kb c-sis mRNA species lacks the strong translation inhibitory potential of the regular exon 1 and contains the code for a PDGF B-like protein that may be targeted to the cell nucleus.

Negative regulation of a special, double AP-1 consensus element in the vimentin promoter: interference by the retinoic acid receptor

The growth-regulated vimentin gene contains a functional double AP-1 binding site formed by two nearly perfect inverted repeats. We present evidence for down-regulation of vimentin expression by the retinoic acid receptor (RAR) in two mesodermally derived cell types. By mutation analysis we prove that the double consensus element is responsible for this negative regulation. From in vitro protein-DNA interaction studies we conclude that AP-1 binding is inhibited at RAR amounts required for occupation of the cognate RAR binding site in nuclear extracts from 3T3 cells and differentiated embryonal carcinoma cells. Furthermore, we show that, unlike in other cases, trans-activation of the vimentin AP-1 enhancer element can occur in undifferentiated embryonal carcinoma cells, despite the low amount of Jun and Fos proteins present in these cells. Here, however, down-regulation by retinoic acid cannot be detected.

Characterization of immunoglobulin G-degrading proteases of Prevotella intermedia and Prevotella nigrescens

Degradation of immunoglobulins is thought to be an important factor in the causation of periodontal diseases by hindering local host defenses and by providing nutrients to the periodontal microflora. In this study, we characterized the proteolytic activity against human immunoglobulin G (IgG) of 20 strains of Prevotella intermedia and Prevotella nigrescens isolated from periodontal pockets and oral abscesses. IgG degradation was studied by sodium dodecyl sulphate-polyacrylamide gel electrophoresis. All strains degraded IgG within 48 h after growth in trypticase-yeast extract medium (TY) supplemented with 0.3% IgG. Incorporating IgG in TY broth enhanced bacterial growth. Protease profiles (zymography), which revealed the presence of 1-4 IgG-degrading proteolytic bands in bacterial cell extracts, became more complex after growth in the presence of IgG. A 38-kDa protease capable of degrading IgG nonspecifically was present in almost all strains. The proteolytic activity was mainly located on the surface of the cell envelope. Two strains of P. intermedia and P. nigrescens ATCC 33563 were selected for further studies. Bacterial cell suspensions in phosphate-buffered saline completely degraded human IgG, IgA and IgM within 24 h. This activity depended on reducing conditions and was inhibited at temperatures above 50 degrees C. The pH optimum of immunoglobulin degradation was at pH 7. Strains cultured at 42 degrees C showed a markedly reduced capacity to degrade IgG. Inhibition studies revealed that breakdown of IgG was caused by a cysteine protease(s). The capacity of P. intermedia and P. nigrescens to degrade immunoglobulins may explain their association with polymicrobial oral diseases.

In vivo footprinting and functional analysis of the human c-sis/PDGF B gene promoter provides evidence for two binding sites for transcriptional activators

By in vivo DMS footprint and reporter gene analyses we identified two transcription factor binding sites in the human c-sis/PDGF B gene promoter. The low basal activity of the PDGF B promoter in HeLa and undifferentiated K562 cells, which express low PDGF B mRNA levels, and in PC3 cells, which express a high PDGF B mRNA level, results from binding of a weak transcriptional activator between positions -64 and -61 relative to the transcription start site. Cytotrophoblast-like JEG-3 cells, which do not express the 3.5 kb PDGF B mRNA, contain a transcriptional activator directed at the -64/-61 sequence, but DNA methylation may render the endogenous promoter inaccessible to this activator. A CCACCCAC element at position -61/-54 was identified as the in vivo binding site for a strong transcriptional activator in phorbol ester-treated megakaryocytic K562 cells, which express a high PDGF B mRNA level. Primary human fibroblasts, which do not transcribe the PDGF B gene, contain a transcriptional activator that recognizes an element between positions -60 and -45 but does not bind to the endogenous unmethylated promoter. Our results show that the complex expression pattern of the human PDGF B gene involves the cell type-specific expression of weak and strong transcriptional activators and regulation of promoter accessibility to these factors.

Degradation of immunoglobulin G by periodontal bacteria

Several subgingival microorganisms were tested for their ability to utilize human immunoglobulin G (IgG) as a substrate for growth. This was done using a protein-free chemically defined medium, supplemented with IgG. Stimulation of growth was observed for Capnocytophaga ochracea, Porphyromonas asaccharolytica, Porphyromonas endodontalis, Porphyromonas gingivalis, Prevotella intermedia, Prevotella oralis, Lactobacillus catenaforme and Streptococcus intermedius. Immunoelectrophoresis, sodium dodecyl sulfate-polyacrylamide gel electrophoresis and a protein assay demonstrated that P. intermedia and P. endodontalis completely degraded the protein chains of IgG. Partial breakdown of IgG was observed for P. asaccharolytica and C. ochracea, whereas P. oralis cleaved the IgG heavy chain, yielding Fc and Fab fragments. All these bacteria utilized IgG as a substrate for growth. Binding studies using an enzyme-linked immunosorbent assay, revealed complete loss of in vitro antigen-antibody binding capacity after incubation of specific IgG with P. endodontalis and partial loss of binding with P. intermedia, P. gingivalis, C. ochracea or Fusobacterium nucleatum. Degradation or inactivation of IgG by oral bacteria is thought to be important in the causation of polymicrobial infections.

A proximal promoter element in the hamster desmin upstream regulatory region is responsible for activation by myogenic determination factors

The muscle-specific intermediate filament protein desmin is up-regulated during skeletal muscle differentiation. When myoblasts leave the cell cycle and fusion into multinucleated myotubes starts, genes associated with myogenesis become activated. The activation is believed to be mediated by the muscle-specific determination factors. We present evidence that both MyoD and myogenin are able to activate the transcription of the hamster desmin gene. A proximal promoter fragment of 89 base pairs is sufficient for this transactivation process. The single E-box in this region is essential for desmin promoter activity in mouse C2 skeletal muscle cells and upon co-transfection of a myogenin expression vector also in human primary fibroblasts. Mutation of this MyoD binding site abrogates desmin transcription, and transactivation of the promoter no longer occurs. By using gel electrophoretic mobility shift assays, we were able to demonstrate that nuclear proteins from C2 muscle cells and myogenin/E12 glutathione S-transferase fusion proteins are able to bind to the functional E-box consensus sequence. A second E-box, situated in a more upstream regulatory region, which also binds to purified Helix-Loop-Helix proteins in vitro is only moderately affected by site-directed in vitro mutagenesis.

DNase-I-hypersensitive sites located far upstream of the human c-sis/PDGF-B gene comap with transcriptional enhancers and a silencer and are preceded by (part of) a new transcription unit

The human c-sis gene encodes the B chain of platelet-derived growth factor (PDGF), a potent mitogen for cultured cells of mesenchymal origin. PDGF is stored in the alpha-granules of blood platelets, which are derived from bone marrow megakaryocytes and lack transcriptional machinery. Human myeloid leukemia cell line K562 can be used as a model for megakaryocytes. Phorbol-ester-mediated megakaryocytic differentiation of K562 cells is accompanied by more than 200-fold increase in the c-sis mRNA level. We have now localized transcriptional enhancers at -8.6 kb and -9.9 kb relative to the human c-sis gene transcription start site. The enhancer at -8.6 kb increases activity of the c-sis promoter by 40-60-fold specifically in K562 cells and comaps with a DNase-I-hypersensitivity (DH) site. The enhancer at -9.9 kb increases c-sis promoter activity by 5-10-fold in K562 cells and DH at that site accompanies phorbol-ester-induced megakaryocytic differentiation. In phorbol-ester-treated K562 cells the two enhancers may be negatively influenced by a silencer that comaps with DH at -10.7/-11.0 kb. Reporter gene analysis predicted that combined activity of the upstream enhancers and the c-sis promoter may result in 100-1000-fold higher promoter activity in phorbol-ester-treated K562 cells compared with untreated cells, which can fully explain the more than 200-fold increase in c-sis mRNA level. DH at -8.6 kb and -9.9 kb was also detected in human fibroblasts and in the carcinoma cell lines HeLa and PC3, which express, respectively, undetectable, low and high levels of c-sis mRNA. Although the individual DH sites displayed 4-10-fold enhancer activity in all these cells, they lost most of their biological activity when combined in a larger fragment. In addition we localized (part of) a new transcription unit at approximately 13 kb upstream of the c-sis transcription start site. The corresponding 0.45-kb sis upstream region (sur) transcript is constitutively expressed in all cell lines examined. The expression of the sur transcript is independent of the expression of c-sis mRNA and of the pattern of DH sites far upstream of the c-sis gene. Thus, at present, there is no indication that the upstream DH sites are involved in regulation of expression of the sur gene.

Localization and functional analysis of DNase-I-hypersensitive sites in the human c-sis/PDGF-B gene transcription unit and its flanking regions

We studied the regulation of the expression of the human c-sis/PDGF-B gene in the following panel of cell lines: K562 cells, in which expression is inducible by phorbol esters; cytotrophoblast-derived cell lines JEG-3 and JAR; carcinoma-derived cell lines PC3, T24 and HeLa, which show extensive differences in c-sis mRNA content; dermal fibroblasts, which do not express the gene. We demonstrate that the wide variety of levels of c-sis mRNA in these cells is mainly determined at the transcription level. Extensive gene rearrangements or amplifications, or significant differences in the stability of the c-sis transcript could not be found. In fibroblasts and placenta cell lines, inaccessibility of the c-sis promoter, rather than the absence of transcription factors that activate it, inhibits expression of the endogenous gene. Examination of the chromatin structure of the transcription unit and immediate flanking regions revealed several cell-type-specific DNase-I-hypersensitivity (DH) sites. Functional analysis of genomic fragments harbouring one or more DH sites showed the presence of negative regulatory elements within intron 1, and of an activating element downstream of the gene. A DH site, located immediately downstream of the promoter in dermal fibroblasts, may regulate accessibility of the promoter by means of specific nucleosome phasing.

Identification of two silencers flanking an AP-1 enhancer in the vimentin promoter

We have studied the 5' upstream sequences required for the transcriptional regulation of the hamster gene encoding the intermediate filament protein, vimentin. Although vimentin is regarded as the intermediate filament protein of mesothelial tissue, it is also produced in most cultured cells. The human mammary carcinoma cell line, MCF-7, belongs to the exceptions. It contains no vimentin, and the complete upstream promoter region is inactive in this particular cell line. By using transient transfection of chimeric constructs into MCF-7 and HeLa cells, and subsequent chloramphenicol acetyltransferase assays, we were able to show the presence of two negative control regions flanking a double AP-1 enhancer element. Our data indicate that these elements exert their effect irrespective of orientation and position, suggesting that they are silencers. In vitro footprinting assays, gel mobility assays and Southwestern (protein-DNA) blotting revealed the presence of trans-acting factors interacting with both silencer elements. The silencing effect was particularly pronounced in MCF-7 cells, although DNA-binding proteins are present in HeLa cells as well.